6Q2K | pdb_00006q2k

The structure of the Streptococcus gordonii surface protein SspB in complex with TEV peptide provides clues to the adherence of oral streptococcal adherence to salivary agglutinin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.235 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

The structure of Streptococcus gordonii surface protein SspB in complex with TEV peptide provides clues to oral streptococcal adherence to salivary agglutinin.

Mieher, J.L.Schormann, N.Purushotham, S.Krishnan, V.B.Wu, R.Patel, M.Wu, H.Deivanayagam, C.

(2026) Infect Immun : e0046725-e0046725

  • DOI: https://doi.org/10.1128/iai.00467-25
  • Primary Citation of Related Structures:  
    6Q2K, 6Q2L

  • PubMed Abstract: 

    Streptococcus gordonii is a commensal bacterium in the oral cavity and has many surface adhesins that have been well characterized. SspA/B belongs to the Antigen I/II-like family of proteins, which are well known for their multifunctional adherence capabilities. Most AgI/II-like proteins adhere to salivary agglutinin (also known as glycoprotein 340, Gp340). In an effort to identify the putative binding site on the AgI/II-like family of proteins, we conducted structural studies to determine the V-domain of SspB. In this paper, we report the structure of SspB's V-domain in complex with a TEV-peptide that was inserted to cleave the histidine tag at the C-terminus after purification. This peptide shared sequence and structural homology with a helical region on the scavenger receptor cysteine-rich (SRCR) domain of Gp340. Our studies with the synthetic peptide PepCD1 SRCR show that it inhibits the Streptococcus mutans biofilm formation in a dose-dependent manner. A comprehensive comparative analysis of this site with the corresponding sites in the homologous V-domains of S. mutans AgI/II and GbpC established that most of these interface residues were conserved. Based on the structural data, mutational analysis was initiated to study the effect of binding-interface residues on the ability of each of these V-domains from S. mutans and S. gordonii to adhere to salivary agglutinin. Here, we report for the first time the binding site for the V-regions that are distinct among oral streptococci, which provides potential opportunities for therapeutic intervention of pathogenic species.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, Alabama, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Agglutinin receptor338Streptococcus gordoniiMutation(s): 0 
Gene Names: ssp5sspB
UniProt
Find proteins for P16952 (Streptococcus gordonii)
Explore P16952 
Go to UniProtKB:  P16952
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16952
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.505α = 90
b = 121.505β = 90
c = 50.745γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2026-03-18
    Changes: Database references, Structure summary